BLAST program selection guide - Cromatina

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BLAST program selection guide HTGS RefSeq RNA RefSeq protein Build RNA Build protein Ab Initio RNA Ab Initio protein ESTs BAC ends Traces-WGS Traces-ESTs Traces-other WGS contigs Gene Trap Clones (Mouse Only) Reference Dog Assembly (boxer) This databases is a collection of all sequences in GenBank that have an HTG keyword. This allows users to search htgs_phase3 sequences (normally found in NR) and htgs_phase0, 1 and 2 sequences (normally found in HTGS) at the same time Collection of reference mRNAs generated by the NCBI RefSeq project. This database is generated daily. Collection of reference proteins generated by the NCBI RefSeq project.This database is generated daily Collection of reference mRNAs generated by NCBI as part of the genome annotation pipeline. This database is generated at the time of a genome release. Collection of reference proteins generated by NCBI as part of the genome annotation pipeline. This database is generated at the time of a genome release. Collection of ab initio RNA predictions generated by NCBI as part of the genome annotation pipeline. This database is generated at the time of a genome release. Collection of ab initio protein predictions generated by NCBI as part of the genome annotation pipeline. This database is generated at the time of a genome release. Single pass sequence reads from cDNA libraries. This database is updated daily. The end sequences of BAC clones. This database is generated daily All of the raw organism WGS traces. This database is updated as needed. All of the raw organism EST traces. This database is updated as needed. All of the raw organism non-WGS and non-EST traces. This database is updated as needed. If an organism was assembled using a whole genome shotgun (WGS) strategy, this database is available (if the WGS assembly is in GenBank). This database is updated as needed. A collection of sequences generated by performing Gene Trap insertions. This database is updated weekly. The supercontigs from the Whole Genome Shotgun (WGS) assembly from a 7.6X coverage whole genome library. This assembly was performed at the Broad Institute using the Arachne assembler http://www.ncbi.nih.gov/staff/tao/BLAST_1.html (4 of 24)12/17/2004 12:36:22 PM
BLAST program selection guide Celera Dog Assembly (Poodle) Celera Dog Extra (Poodle) Ref Chimp Assembly Alt Chimp Assembly Celera CSA Celera cWGA Celera WGA This database is a collection of the Whole Genome Shotgun (WGS) contigs assembled from a 1.5X coverage whole genome library. A description of this assembly can be found in Kirkness et al (2003). This database a collection of Whole Genome Shotgun (WGS) reads that were not assembled into contigs (the Celera Dog Assembly). A description of the assembly can be found in Kirkness et al (2003). This database a collection of Whole Genome Shotgun (WGS) contig assemblid using the program Arachne. These contigs were assembled from a 4.5X coverage set of WGS reads.A publication describing this data should occur in early 2004 This database a collection of Whole Genome Shotgun (WGS) contig assemblid using the program PCAP. These contigs were assembled from a 4.5X coverage set of WGS reads.A publication describing this data should occur in early 2004 Celera January 2001 compartmental shotgun assembly (CSA) of the human genome. It was generated from the 27 million reads of Celera's 5.3X whole genome shotgun data and 16 million 'reads' of shredded GenBank data from other human genome projects ( Nature 2001. 409:860-921). It was generated by the Celera Assembler applied to 3800 separate compartments of Celera and GenBank data associated by inferred sequence overlaps and Celera read pairs. It relied on Celera's paired reads and the BAC end reads for long range order and orientation. See Istrail et al (2004). This is the November 2000 combined whole genome shotgun assembly (WGA) of the human genome. It was generated by the Celera Assembler applied to the 27 million reads of Celera's 5.3X whole genome shotgun data and 16 million 'reads' of shredded GenBank data from other human genome projects ( Nature 2001. 409:860-921). It relied on Celera's paired reads and BAC end reads from GenBank for long range order and orientation. See Istrail et al (2004). This is the December 2001 whole genome shotgun assembly (WGSA) of the human genome. It was generated by the Celera Assembler applied to shotgun data only: the 27 million reads of Celera's 5.3X whole genome shotgun data and 104,000 BAC end sequence pairs from GenBank from other human genome projects (Nature 1996. 381:364-366; Genomics 2000. 63:321-332). It relied on Celera's paired reads and the BAC end reads for long range order and orientation. See Istrail et al (2004). http://www.ncbi.nih.gov/staff/tao/BLAST_1.html (5 of 24)12/17/2004 12:36:22 PM
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BLAST program selection guide - Cromatina

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